Man pages for DIscBIO
A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
| as.DISCBIO | Convert Single Cell Data Objects to DISCBIO. |
| check.format | Check format |
| ClassVectoringDT | Generating a class vector to be used for the decision tree... |
| ClustDiffGenes | ClustDiffGenes |
| Clustexp | Clustering of single-cell transcriptome data |
| clustheatmap | Plotting clusters in a heatmap representation of the cell... |
| comptSNE | Computing tSNE |
| customConvertFeats | Automatic Feature Id Conversion. |
| DEGanalysis | Determining differentially expressed genes (DEGs) between all... |
| DEGanalysis2clust | Determining differentially expressed genes (DEGs) between two... |
| DISCBIO | The DISCBIO Class |
| DISCBIO2SingleCellExperiment | Convert a DISCBIO object to a SingleCellExperiment. |
| Exprmclust | Performing Model-based clustering on expression values |
| FinalPreprocessing | Final Preprocessing |
| FindOutliers | Inference of outlier cells |
| foldchange.seq.twoclass.unpaired | Foldchange of twoclass unpaired sequencing data |
| HumanMouseGeneIds | Human and Mouse Gene Identifiers. |
| J48DT | J48 Decision Tree |
| J48DTeval | Evaluating the performance of the J48 decision tree. |
| Jaccard | Jaccard’s similarity |
| KmeanOrder | Pseudo-time ordering based on k-means clusters |
| NetAnalysis | Networking analysis. |
| Networking | Plotting the network. |
| NoiseFiltering | Noise Filtering |
| Normalizedata | Normalizing and filtering |
| PCAplotSymbols | Plot PCA symbols |
| plotExptSNE | Highlighting gene expression in the t-SNE map |
| plotGap | Plotting Gap Statistics |
| plotLabelstSNE | tSNE map with labels |
| PlotMBpca | Plotting pseudo-time ordering or gene expression in... |
| PlotmclustMB | Plotting the Model-based clusters in PCA. |
| plotOrderTsne | Plotting the pseudo-time ordering in the t-SNE map |
| plotSilhouette | Silhouette Plot for K-means clustering |
| plotSymbolstSNE | tSNE map for K-means clustering with symbols |
| plottSNE | tSNE map |
| PPI | Defining protein-protein interactions (PPI) over a list of... |
| prepExampleDataset | Prepare Example Dataset |
| pseudoTimeOrdering | Pseudo-time ordering |
| rankcols | Rank columns |
| reformatSiggenes | Reformat Siggenes Table |
| replaceDecimals | Replace Decimals |
| resa | Resampling |
| retrieveURL | Retries a URL |
| RpartDT | RPART Decision Tree |
| RpartEVAL | Evaluating the performance of the RPART Decision Tree. |
| sammy | Significance analysis of microarrays |
| samr.estimate.depth | Estimate sequencing depths |
| valuesG1msTest | Single-cells data from a myxoid liposarcoma cell line |
| VolcanoPlot | Volcano Plot |
| wilcoxon.unpaired.seq.func | Twoclass Wilcoxon statistics |
